Twelve
by AlexWayne
Summary: When a fatally wounded Eleventh Doctor is forced to regenerate, an unexpected issue is brought to light. Reviews are welcome!
1. Out of Time

The Eleventh Doctor ran, clutching his side, stumbling as the explosions rang all around him. He fell in through the doors of the TARDIS and collapsed on the spot, unable to move anymore.

He began to close his eyes.

"You're not done yet, doc!" Jack yelled, firing his gun over his shoulder before dragging the Doctor by the arms.

Slamming the doors shut, Jack sighed before pulling the Doctor to his feet.

"There you go, take it easy…" Jack replied soothingly.

"Jack…? What…what are you doing here…?" The Doctor blinked rapidly.

"Heard you were traveling alone these days, thought I'd come see your new face," Jack grinned.

The Doctor smiled and took a step forward before his knees gave out and he fell to the floor.

"Whoa, take it slow, tiger…" Jack came to his aid.

Looking at the gash on the Doctor's side, Jack relaxed a bit.

"It looks pretty superficial…nothing fatal…the cut isn't real deep."

The Doctor smiled sadly.

"Just after I managed to escape having my molecular biology completely rewritten I found myself in a sword fight…unfortunately the sword was laced with poison…I…don't think you will get to see this face for much longer…"

Jack inched forward.

"But you can handle poisons can't you? You've done it before."

"Poisons that affect humans, yes, but this…I was not prepared for this…" The doctor replied quietly.

He groaned and snapped his eyes shut.

"Is there no antidote?" Jack quickly asked, instinctively putting a hand on the Doctor's shoulder.

"I don't know…I've never felt something like this…the pain…" He swallowed and his eyes rolled back a moment, "…the pain is terrible…even if there was something I could do…there's no time, Jack…no time…"

Jack nodded solemnly before tucking his hands under the Doctor's arms to pull him back to his feet, allowing him to lean on his shoulder.

"I've never seen you give in…" Jack looked into his eyes, "What changed?"

"A lot has happened these last few years…" The Doctor looked at nothing in particular and seemed to be lost in thought.

A blast brought him back to reality.

"They're trying to break in!" Jack's eyes widened as he stared at the TARDIS doors.

The Doctor ran from Jack's arms and began pressing buttons and pulling levers as he ran around the circular control center, his eyes locked in a determined stare with the panel until one final switch brought the familiar roar as the TARDIS sprang to life, screeching with the iconic sound as the machine dematerialized in front of its attackers.

The Doctor stood back with a triumphant grin spreading across his features.

"There he is…" Jack smiled back, catching his eye. "The Doctor I know!"

The Doctor's smile quickly faded as a wave of pain blinded him and sent him crashing against the control panel.

"Jack…get me to the medical bay...please" He yelled, closing his eyes and groaning. "I'm out of time…"

Jack sprinted over and half carried the Doctor down the corridor to the med center. Pulling him onto a gurney, Jack looked down sadly as the Doctor's hearts sped up from the strain.

"Can I get you something for the pain, doc?"

"Yeah…next room over…in the top left cabinet…a blue bottle…quickly…"

Jack flew out of the room and burst through the doors, flinging the cabinet open and knocking bottles away before finding two blue bottles. One had white pills while the other one had a slight pink tint with purple spots across them.

"Which one?" Jack panicked as he heard the Doctor yell in the next room.

Grabbing both he decided he would ask when he got there.

He was just about to run back to the Doctor when a blinding light shown through the window on the door, casting an eerie yet beautiful yellow glow on Jack as he shielded his eyes.

"Doctor…?" Jack reached carefully for the door handle when it was over.

"Don't come in!" A voice yelled from inside.

It sounded higher than the Doctor's voice, but his was likely to change octaves after regeneration.

"Are you alright?" Jack tried to peak inside but upon spotting the gurney, he noticed it was empty.

Pushing the door open quietly, Jack snuck inside. As soon as the door snapped shut, the Doctor popped up from behind the gurney and Jack knew he was mad, but couldn't contain the shock of the new form before him.

"What part of 'don't come in' didn't you understand?!" The Doctor screamed.

Jack's mouth was hanging wide open and for the first time, he was speechless.

"Stop staring…" The Doctor groaned.

"But you…"

"Don't say it!"

"You-"

The Doctor shot a warning glance.

"You look stunning, doc…" Jack replied.

"I need a mirror…" The Doctor mumbled, shoving past Jack and running from the room.

While Jack stayed behind a sudden scream echoed from down the hallway.

Jack ran towards the sound and found the Doctor, mouth open and hands clutching hair, in front of a mirror, opening and closing his mouth trying to speak.

"Jack…" he croaked.

"I know…"

"Jack!" he spun to face the captain.

Jack smiled sadly and tried to mask the excitement he really felt.

"I'm female, Jack…" The Doctor whispered.


	2. A New Face

Chapter 2

The Doctor kept closing his eyes, or _her _eyes only to open them in front of the mirror and find that it was true.

"How-wh-how did this…" She trailed off. "No…"

Her eyes widened with realization and she began talking a mile a minute.

"The molecular biology! They must have done enough damage before I got away, my chromosomes were in limbo for a while but was that really enough for them to change? No. Yes? No! That can't be…" She looked in the mirror again, "When I regenerated, the mix-up must have caused a mutation, changing my gender…is that even possible…?"

"Well you look amazing!" Jack chimed in, looking the Doctor up and down.

Frowning, she turned to the mirror and looked at herself.

She _was _very good looking.

She was a medium height girl with long flowing auburn hair, bright green eyes lit with feistiness, light freckles dotted beneath her eyes. Her dark lashes making her freckles and eye color stand out even more. She was thin but muscular, giving her a look that meant she could take care of herself without appearing brutish. She looked ridiculous in the tweed jacket and the bowtie that still wrapped around her collar was now hanging loosely around her tiny neck.

Overall she was impressed with her pretty new image, but then the realization of the situation donned on her and she frowned.

"Jack…I'm a girl…" she groaned.

"Count your lucky stars, doc, you look hot…" Jack replied.

She cringed.

"What am I going to do now?" She threw her hands up in the air, frustrated.

"…What do you mean…?"

"Do you realize how restrictive it is to be a female in the history of the universe?"

Jack remained silent.

"There are entire time periods of Earth and even whole planets that did not or still do not like women!" She explained.

"Guess it makes you appreciate what all of your companions have gone through…"

"Exact-Hey…"

The Doctor glared at Jack but he just smiled.

"I appreciate everything they went through," she explained, "I have never not been thankful for all they have done for me…but that was different! I was around to make sure nothing happened to them! There is only so much authority I can command like this…"

"I guess you will have to settle for being _my _companion a while, doc…" Jack smirked.

She took a step back.

"What are you talking about…?"

"Well," Jack mimicked the way the tenth regeneration would whip his head around while beginning an explanation, "I can handle the authoritative front while you can safely be the brains behind our little adventures…it'll be like old times, us working together, but I'll be the muscle for ya!"

The Doctor tilted her head to the side before shrugging and giving in.

She turned to give herself another look in the mirror and paused for a moment. She ran a hand through her hair, making it messier than it already was, and her brow creased with concentration as she tried to fix herself up.

"Oh, Doctor, please, allow me…" Jack grabbed the Doctor and led her to the enormous closet containing all the outfits of his previous regenerations and more. Jack practically skipped over to where some of the companions had left dresses.

"Doctor, I have been waiting for this moment my whole life…" He grabbed a revealing black dress from the rack and held it up for the Doctor's approval.

"No," she replied simply.

Jack grabbed a backless red dress with a streak of sparkling silver running down the side.

"No, no dresses!" The Doctor called out, "Especially not ones like _that_."

Jack rolled his eyes and rubbed his brow. "Your sense of style is gonna need some work…"

The Doctor took Jack by the arm and gently ushered him out of the room with a polite smile before slamming the door in his face.

"I'll pick my _own _style thanks…"

She scanned the isles for the perfect outfit. She knew she wouldn't be able to get away with wearing anything so masculine as _he _had in the past, but she refused to wear anything too feminine.

XXXXXXXXXXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXX

Jack was pacing around the control room, still trying to wrap his mind around the Doctor's new appearance when she reemerged from behind the closed door.

Jack was taken aback.

She was wearing skinny black military-style pants, with a belt containing small gadgets, not the least of which was the screwdriver. Her black boots were laced up her shins, giving her a uniform appearance. On top she had a blue military jacket that would button all the way up into the collar but instead, it was open, exposing a white, fitting blouse. She looked fiery and determined and Jack was practically head-over-heels as she stood there waiting for his approval. Jack scanned her head to toe and back up again before realizing that while her messy auburn gave her a sexy, naughty look, no one would take her seriously.

As a friend, Jack decided to point it out, rather than leave it for his own pleasure.

"Here…" he began reluctantly as he walked over.

At first, the Doctor did not want Jack to touch her hair but feeling it would be quicker to just give in, she waited patiently while he pulled and played around with her hair. As soon as he was finished, Jack smiled pleasantly and gestured to the mirror.

Hesitantly, the Doctor walked over and was immensely relieved by what she saw.

Her flowing auburn hair had been tamed in a long silky braid that ran down her shoulder blades and while making her beautiful, it only added to her level of intensity. She successfully gave herself a look that meant she was not to be messed with. And she wasn't…

She was the Doctor.


	3. Old Friends

Chapter 3

"Why is it so important to go see her?" Jack asked as the TARDIS landed inside the old warehouse.

"Because I'm going to need all the help I can get…" The Doctor replied, stepping though the doors and smelling the fresh air.

She smiled and closed her eyes before snapping them open and studying Jack up and down with a growing frown on her face.

"I feel shorter…am I much shorter…?" She asked.

Jack walked up next to her and it was the first time she noticed the height difference.

"What are you…? 1.8 meters…?"

Jack shrugged.

"I can't be more than 1.7…I feel short" She replied, standing up straight.

Jack just laughed and started walking towards double doors leading out of the warehouse.

Suddenly, a young man in a uniform and red beret appeared and pointed his gun at them.

"Whoa!" The Doctor exclaimed, "There is no need for that! Look," She reached for her psychic paper.

"Don't move, lady!" The man yelled, "Who are you?" He asked, addressing Jack only.

"I'm the Doctor…" She said, calmly.

The man shot her a rude look, "Was I talking to you?"

"I'm Captain Jack Harkness…" Jack began, drawing his attention back. "We are here to see Dr. Martha Jones…this is UNIT headquarters isn't it?"

"Yes, how did you get in?" The man continued, not letting his guard down.

"We dug a hole from China," The Doctor replied, snidely.

The man's eyes darkened but she didn't turn away.

"Look, can we see her or not? We're friends of Dr. Jones and I personally Lieutenant Davies…do you want to call him up and check?" Jack challenged.

The man paused a moment, his eyes wandered over to the Doctor who was still giving him a death stare.

"This way…" The man backed down and led them towards the main building at the heart of the base.

Upon entering the building, all of the uniform-clad men and women turned their heads as the two walked past. A few men in lab coats talking over a coffee machine became quiet and one pointed towards Jack and the Doctor. Jack seemed to be enjoying the attention wave that crashed over the workers; he even smiled at one particularly muscular armed man, who, the Doctor swore, blushed a little. The Doctor herself was feeling very uncomfortable. She was never comfortable with the stares and recognition she had gotten for being the Doctor but this was entirely invasive. Many of the soldiers were whispering among themselves with cheeky grins and one even winked as she walked past. She felt disgusted and suddenly wished she could be in a room with all of her previous companions to tell them she was sorry that this ever might have happened to them.

When the show was over, the workers resumed their task and Jack and the Doctor were mercifully hidden away behind large double doors. Just as they entered the room, the Doctor recognized Lt. Davies and the man next to him, Sgt. Walker.

"Davies!" Jack exclaimed, pulling him into an embrace.

"Jack!" He responded as enthusiastically. "How are you?"

"Oh I'm great, haven't been up to see you guys in a while! Oh Corporal Walker!" Jack continued.

"He's a sergeant now, Jack…" The Doctor joined in, smiling.

Sgt. Walker smiled at the Doctor before turning his attention to Jack.

"It's true. Although, I was not expecting to have such a beautiful fan…"

The Doctor turned away, flushing with embarrassment.

"I often have that effect on women…" Walker joked, grinning at the Doctor.

"Oh, I hope not, Jim…pay her no attention, she doesn't swing that way…" Jack began with a wave of his hand.

The Doctor's face drained of color but she had no idea how to counter that. She supposed he was doing her a favor, but only just.

"Awe, what a shame…all the prettiest ones are, aren't they?" Jim Walker asked Jack.

"You could say that…" Jack laughed.

"What's your name?" Davies cut in.

"Jo-Joan…Joan Smith…" The Doctor replied.

"Joan? I know a Joanie, she's a great girl…" Davies faded away in thought.

"Joan." The Doctor added quickly. "Not Joanie…"

No one was paying her any attention though but continued swapping stories about the past several years. After a good twenty minutes of chatter, the Doctor finally grew impatient.

"So!" She loudly interrupted, "When is Martha Jones due in?"

The men stopped talking and Davies shuffled around, acting like a scolded child.

"I'll call her down," Walker pulled out his walkie and called someone names Thompson to see if Martha was available. Thankfully she was.

"Now, back to that trip to Mumbai…" Walker continued.

"Where's the loo?" The Doctor cut in.

The three turned their attention to her and Davies stepped up.

"This way," he gestured, heading out the door.

She was thrilled to no longer be shooed away while the others talked of adventure. Many of which were extremely dull compared to the list of excitement she had had. Davies turned on a light and stood aside to let her enter but before she could shut the door, he was practically on top of her. Their faces were inches apart and while the Doctor tried to back up, she found herself pinned up against a cabinet.

"I don't buy the story about you only going for women…someone this pretty…" He leaned in to kiss her.

Shoving his face away, she immediately tried to explain.

"Davies…I swear, Jack was telling the truth…"

"You lie," he smiled, running his tongue over his teeth.

He hearts sped up like a freight train when he leaned in again.

Despite her pleading, Davies wasn't going to stop.

"I…I'm dating Jack Harkness!" She cried, pressing the back of her head against the cabinets, as far away from him as she could get.

Davies stopped, his lips still puckered.

"…wait…what…?" He pulled back, allowing the Doctor to exhale with relief.

"Yes! We are dating! He didn't want anyone to know because he doesn't usually do steady relationships…and well…we are engaged…so I can't be…this…"

Davies took a step back and let his face fall into his hands.

"Oh…god…" Davies muttered into his hands, "Jack is going to kill me…I didn't know you were his girl!"

"It surprises me a bit as well…" The Doctor replied, sliding over to the side, creating more space between them.

"I'm so sorry, Joanie!" Davies reappeared from behind his hands.

Ignoring the name, the Doctor took a deep breath as Davies began again.

"I read the signals all wrong…I thought-"

"Signals?!" The Doctor spat, "What 'signals' were you picking up?!"

"I thought the bathroom was a cover!"

The Doctor allowed her mouth to open as she walked out of the room, leaving Davies without another word.

When she came back to the room, Jack noticed her traumatized expression and grew more concerned when he saw Davies, pale as a ghost, slink away down the hall. Jack quickly ran to the Doctor and tried to read her eyes for a clue of what had just occurred.

"What happened…?" Jack put a hand on the Doctor's shoulder.

"Davies cornered me in the john and tried to kiss me…apparently I was giving him 'signals'…" she made the quote sign with her hands.

Jack was caught between feeling bad and laughing.

"Maybe you are wishing you were slightly less good looking now, huh?" Jack grinned.

The Doctor couldn't help but laugh.

"The only nice thing is I may have traumatized Davies, and now he thinks you will kill because the only way to get him to back down without violence was to make him think we were dating. He's convinced you will hate him now."

"Well, he can suffer with that thought for a while…" Jack added with a sneaky grin.

"Jack?" A familiar voice broke though their laughs.

Both the Doctor and Jack turned and saw Martha Jones standing in the doorway.


	4. Trust Me

Chapter 4

"Martha!" Jack shouted as he ran up and hugged her, swinging her around.

"Easy, there," Martha replied when he put her down. "What are you doing here?"

"You are not going to believe this…" Jack smiled and pointed towards the Doctor.

She smiled friendly but was held back by her new appearance and could not give Martha a hug as Jack had done.

"Hello, I'm Martha Jones, and you are?" Martha extended her hand to the Doctor.

The Doctor shook it and searched for the words to explain what had happened.

By this time, Davies had returned. His strange attitude had not gone unnoticed by Walker, who was leaning in, asking what was wrong.

"Um…" The Doctor began, expecting Martha to loose interest.

Much to the Doctor's excitement, she smiled in an understanding fashion.

"It's okay, would you like a drink, ma'am?" She asked politely.

"I really wish you wouldn't call me ma'am…" The Doctor began, "Okay…I'm just going to come out and say it…" she stared into Martha's kind brown eyes.

The Doctor had never been eye-level with her before, this height issue was going to take some getting used to.

"It's me…the Doctor…"

Martha's smile faded and she looked to Jack, expecting him to laugh and confirm that this was in fact just a joke.

He only nodded.

"I know…" The Doctor continued quickly, "I still can believe it myself but look," she grabbed Martha's hand and held it to her first heart, and then her second, ignoring the feeling of awkward placement the Doctor had never felt before. "It's me."

Martha's mouth dropped open and she stepped back so the Doctor tried to keep explaining.

"It's a long story but I regenerated once and wore bowties for a while, and a fez! I loved that fez. But I died a second time since we saw each other and it was after I was kidnapped by some 67th century humans who wanted to rewrite my molecular structure, much like I did to myself when I was human, remember the family of blood? Anyway, they were in the process of doing something similar but I escaped, barely, but I was injured. Jack was there, he'll tell you all about it. But then I died and when I regenerated, something had gone all wonky and now I'm female. It's really not been a pleasant experience but I swear to you this is not a joke. I made Jack bring me to you because I didn't know what else to do…"

Martha closed her mouth but remained silent.

"I don't know what else you want me to say to prove it…" The Doctor added, "You took care of me when I was human, your mum hates me, The Master imprisoned your family during The Year but not you, no! You are the Girl Who Walked The Earth! We faced The Angels, The Daleks in Manhattan, we met Shakespeare and Queen Elizabeth before being chased from the Globe, you saved my life countless times…as we were falling into the sun, for starters, and you saved the whole planet from the Master when you walked the Earth…helped stop the Atmos from killing everyone, I could go on and on…"

She smiled at Martha who slowly began to smile back.

"Doctor…?" Martha had tears brimming her eyes.

The Doctor smiled.

Martha leapt forward and pulled the Doctor into squeezing hug and closed her eyes tightly.

"Oh, I've missed you!" She exclaimed.

"You don't mind hugging me…? You know…as a girl…?"

Martha pulled back and looked her up and down.

"Sometimes you are really thick…has anyone ever told you that?"

"Never," she replied sarcastically.

"That little line convinced me even more than listing all of those things…you are still the same…" Martha grinned.

The Doctor laughed and took a step back, flattening a wrinkle in her jacket.

"Not totally the same…" She chuckled.

At that moment she saw the horrified look on Davies' face.

"Doctor…?" He squeaked.

"Hello, Sam." She smiled mischievously.

All color disappeared from his face as he ran from the room.

"He's traumatized now…" The Doctor smiled to Jack.


End file.
